Proposal to the USGS-NBII

Cover letter

From: John Pickering <pick@discoverlife.org>
To: Annie Simpson <asimpson@usgs.gov>

27 November, 2003

Annie Simpson
National Biological Information Infrastructure
USGS

Annie,

Here is our proposal for FY2003-4 totaling $80,000. The first part is to develop IDnature guides to vertebrates and trees of North America, including native species, known alien invasive species, and exotic species that are commonly available as pets and ornamentals. The final part is to assess how we should integrate the current reporting and mapping tools on Discover Life and Topozone.com so that they best meet the needs of different agencies and organizations that want the public to help them detect, map, and monitor invasive species. If it meets your approval, please relay it to Gladys. If not, send me your recommendations, and I'll change it.

Cheers,
Pick

________________________________________________________
John Pickering	Office: 706-542-1115
717A Biological Sciences Building	FAX: 706-542-3344
University of Georgia	Lab.: 706-542-6676
Athens, GA 30602-2602	Department: 706-542-3379
e-mail: pick@discoverlife.org	Home: 706-353-7076
URL: <http://www.discoverlife.org/who/Pickering,_John.html>
________________________________________________________

Proposal

Title: Web tools to identify, report, and map invasive species in North America.

Principal Investigator: John Pickering, University of Georgia, Athens

Administrative Contact: Kevin Weick, The Polistes Foundation,
       <http://www.discoverlife.org/who/Weick,_Kevin.html>

Summary: We are developing technology to overcome the two major hurdles that greatly impeded citizens from contributing to the study and management of biological diversity and other natural resources. Many schools and volunteer organizations could help detect and manage invasive species, for example, simply by studying nature in their local communities and reporting what they find. However, most are prevented from contributing valuable data. They lack the ability to identify target species reliably and cannot easily share their findings with others. They need identification guides that are illustrated, non-technical, and can be successfully used by beginners with minimal training. They need intuitive data reporting tools that empower novice users to locate their study sites accurately, database their findings, and exchange high-quality information through maps that filter data by source and reliability.

Here we propose to continue building interactive guides that will help users identify invasive species in North America. Specifically, we will develop IDnature guides to 2,500 vertebrates and trees of North America, including native species, known alien invasive species, and exotic species that are commonly available as pets and ornamentals. We will make these products freely available to Web users through Discover Life (http://www.discoverlife.org). They will give teachers, students, citizen scientists, land managers, and scientists alike powerful tools to distinguish invasive species from each other and from their native look-alikes.

Discover Life, in partnership with Topozone.com, has developed Web tools to report and map information about species. The final part of this proposal is to assess how we should integrate these tools and the IDnature guides so that they best meet the needs of agencies and organizations that want the public to help them detect, map, and monitor invasive species. We propose to hold a workshop to evaluate existing technology and recommend how it should be improved. In addition, we propose to work with the Balsam Mountain Trust and two county school districts in western North Carolina as a test bed of this technology, using students and volunteers to tell us from their perspective what works, what needs to be fixed, and what new features they would like added.

We propose to do the following:

1. Guides
   Using The Polistes Corporation's 20q software (http://www.discoverlife.org/nh/id), we propose to build IDnature guides to distinguish invasive species from each other, from their native North American look-alikes, and from common exotic pets and ornamentals.
   • We propose to enhance existing checklists and guides so that users can identify 2,500 kinds of vertebrates and trees in North America, including:
     • Birds -- 1,200 kinds, including distinctions by sex, age, region, and season
       (http://pick4.pick.uga.edu/mp/20q?guide=Birds),
       
     • Frogs & Toads -- 102 kinds, including subspecies
       (http://pick4.pick.uga.edu/mp/20q?guide=Anura),
       
     • Trees -- all common native trees and some important shrubs
       (http://pick4.pick.uga.edu/mp/20q?guide=Plants),
       
     • Salamanders -- 70 kinds
       (http://pick4.pick.uga.edu/mp/20q?guide=Salamanders),
       
     • Snakes -- 300 kinds, including subspecies
       (http://pick4.pick.uga.edu/mp/20q?guide=Snakes),
       
     • Turtles -- 50 kinds
       (http://pick4.pick.uga.edu/mp/20q?guide=Turtles).
       
     If resources permit, we will also start guides to mammals (http://pick4.pick.uga.edu/mp/20q?guide=Mammalia)
     and fish. Where appropriate, the guides will distinguish different sexes, seasonal morphs, and different life stages, such as eggs, juveniles, adults, fruits, seeds, flowers, etc.
   • We will select the species from the checklist that we maintain at http://www.discoverlife.org/nh/tx/INVASIVES, adding new species as requested by NBII. Started in 2002, this checklist currently links to information on 250 kinds of invasives.
   • We will put trees and shrubs into an integrated plant guide that currently includes over 1,000 Wildflowers that Kay Yatskievych and her volunteers at Missouri Botanical Gardens have added. Eventually this guide will include ferns, grasses, and other plants. Our illustrators and technical staff will provide general support to Missouri Botanical Garden and other partner organizations that contribute to guide building.
   • The proposed guides' underlying data structure will be in XML, as specified in by the schema for IDnature guides at
     http://www.discoverlife.org/ed/tg/Building_Web_Pages/20q_xml_tags.html
     These XML files will be put on Discover Life and made available to everyone through the software's export_xml function under Menu.
   • We will build one master guide to vertebrates and subguides as appropriate. The structure will follow the one we built for Butterflies that draws information from XML files for each butterfly family using the above schema's <include> tags. For this example guide, please see
     http://pick4.pick.uga.edu/mp/20q?guide=Butterflies.
   • The proposed guides will include scientific names, other names, character-state attributes used in identification, illustrations of character-states, and links to images and information about each species.
   • Nancy Lowe (http://www.discoverlife.org/who/Lowe,_Nancy.html), Cheryl Reese (http://www.discoverlife.org/who/Reese,_Cheryl.html), and other artists will illustrate the morphological character-states in the proposed guides. The guides will present their illustrations as thumbnails that link to higher resolution images. John Pickering will retain ownership and copyright of these illustrations. The public will be allowed to use them for non-profit purposes so long as they credit the illustrator and specify a link to Discover Life where used.
   • Technicians will support the proposal by processing images, scoring attributes, and linking the guides to images and information for each species. They will try to link each species in the guides to at least one high-quality photograph, a distribution map, textual information from fact sheets, such as from the Global Invasive Species Database, and taxonomy from ITIS.
   • Where appropriate the guides will distinguish kinds within species, allowing users to identify distinct kinds to sex, age, region, seasonal characters, and life stages. For species that cannot be distinguished by field markings, the guides will resolve identifications to all possible species or to a higher category that includes a species.

2. Reporting & mapping
   The Polistes Foundation and its partners support the development of Discover Life and its suite of software tools and linked databases that collect, integrate, and share information globally. To help monitor and manage alien invasives, we plan to allow everyone to integrate time-sensitive, geo-spatial information into real-time maps, whether contributors be institutional databases, students reporting findings from their class projects, or individual volunteers.

   If data were current, rather than often months or years out-of-date, the fine-grain accuracy of Topozone.com's topographic maps and aerial photographs would greatly aid local managers in coordinating early detection and rapid response to invasives. At larger scales, up-to-date global and regional maps would better alert quarantine inspectors and trade policy makers to potential dangers associated with movement across borders.

   Discover Life currently overlays spatial information from institutional databases, such as Missouri's Tropicos, onto maps and aerial photographs served by Topozone.com. Points on these maps link users to corresponding database records. Our on-going 2003 NBII proposal includes the integration of up to 20 institutional databases into this mapping system, as discussed below in section 3, "Global Mapper & institutional databases."

   Here we propose a workshop and prototype to determine how to extend our existing tools into a real-time system that will let all Web users report geo-referenced data and map their collective effort.

   • WORKSHOP -- to evaluate existing on-line reporting and mapping tools, to prioritize the functions users need to report and map invasive species, and to anticipate pitfalls and possible solutions.

     We propose to organize a 2-day workshop as soon as possible, ideally associated with a related meeting, such as the Global Invasive Species Information Network workshop in April, 2004. Alternatively, we will host the workshop at either Harvard University, the University of Georgia, or near Balsam Mountain, the prototype site in North Carolina proposed below.

     We propose a workshop of about 20 individuals representing

     • Data users: agencies and organizations concerned with invasive species, including representatives from the U. S. Invasive Species Council, GISIN/Global Invasive Species Program, and the International Plant Protection Convention,
     • Educators & other data providers: programs and organizations that could organize individuals to participate, contribute data, and learn from their experience, such as Balsam Mountain Trust, First Hand Learning, GLOBE, Great Smoky Mountains National Park's ATBI, Massachusetts Biodiversity Days, Missouri Botanical Garden, Roots & Shoots, and
     • Technical experts & scientists with experience in research methods, taxonomy, Web reporting, data quality assurance, and mapping, including the BioNET International, Cornell Ornithological Lab, ITIS, Massachusetts Biodiversity Days, Nature Mapping, NatureServe, Topozone.com, and USGS (Breeding Bird Survey; Frog Watch).

     The agenda will address issues that include:

     • Needs of data users: research design and protocols, which fields of data to collect, accuracy required, etc.
     • Needs of data providers: learning experience, training required, data ownership, what data may be shared, what must be kept private (e.g., reports on rare and endangered species), etc.
     • Technical issues: security, data quality assurance, how to distribute information to users, integration with other efforts, etc.
     • Action plan: outline next steps

   • PROTOTYPE -- to identify and evaluate the functions and pitfalls associated with Web-based reporting of invasive species.

     We propose to develop prototype sites with the Balsam Mountain Trust, Balsam Mountain Preserve, and two county school districts in western North Carolina. The Balsam Mountain Trust is a 501(c)(3) organization and serves as the daily environmental conscience of the 4,400 acre Balsam Mountain Preserve. One of their challanges is in their riparian zone along 15 miles of permanent streams and 23 miles of intermittent streams. They wish to save an estimated 2,800 hemlock trees from destruction by an alien invasive pest, the Hemlock Wooly Adelgid, Adelges tsugae. Because they, as private land owners, do not have access to the limited supply of predatory beetles that are slated for public lands, their land managers plan to save their hemlocks from the adelgids with chemical rather than biological control. Unfortunately, this solution is costly and could create run-off that would pollute the streams, threatening native brook trout that are in them along with over 300 other species linked to the hemlock community.

     The Trust's Director, Cherie Pittillo, and Senior Naturalist, Michael Skinner, are working with numerous agencies and universities to help them manage their land wisely. Before it is too late for another tree species, they also want to educate the public about this invasive insect, how to identify it and its host, the different treatment methods available to the public, and how to use them safely. They have established 13 water quality monitoring stations with two years of baseline data, have installed four 20 x 50 meter permanent Gauss hemlock forest plots to monitor the inpact of the adelgids with Western Carolina University, installed 23 other permanent plots in different plant communities at different elevations for monitoring, and have started a two year Aquatic Insect Survey with Clemson University.

     In partnership with the Balsam Mountain Trust and their local schools, we propose to

     • develop an IDnature guide that allows high school students to identify hemlocks, adelgids, and other species associated with these trees,
     • develop a custom reporting tool that will allow students to map and monitor hemlocks for adelgid density and other variables that the students wish to investigate,
     • design an experiment and research protocols that will allow students to monitor the hemlocks and assess the pros and cons of chemical application on some trees and not on others,
     • evaluate the accuracy of the data collected,
     • modify the identification, reporting, and mapping tools based on what we learn in this study,
     • make the modified reporting system and data available to other organizations working with adelgids in the area, such as SAMAB/SAIN and Great Smoky Mountains National Park.

   We will use feedback from the workshop and prototype to prioritize a scope-of-work that will be used to continue the project and develop real-time Web tools to allow the world community to contribute to the study, mapping, and control invasive species.

3. Global Mapper & institutional databases
   As part of our on-going 2003 grant from NBII, we proposed to integrate spatial point data into distribution maps for up to 20 Web-enabled databases that NBII selects and get authorization from their owners. Should NBII not be able to reach this target by the end of the 2003 grant, we here extend through the current proposal our offer to map data from up to 20 databases.

   Technical details of the Global Mapper, Topozone.com, and linking database are as follows:

   • We enable Web users to build and display maps with 20q's Global Mapper (see http://pick4.pick.uga.edu/mp/20m.) This mapper is developed by the partnership between Topozone.com (see http://topozone.com) and The Polistes Corporation. It plots points on a composite satellite image of the globe and then allows users to zoom in through various layers to see detailed maps. Currently its base maps include a 1:1,000,000 scale map of the world, 17 million topo maps of the United States, and aerial photographs of 89% of the United States to 1 meter per pixel resolution. In total, approximately 20 terabytes of data reside on Topozone's servers and are used by the Global Mapper.
   • In addition to clicking on the satellite image from livingearth.com to zoom in on a place on the globe, the Mapper's banner includes the following four options:
     • Help -- explains how to use the Mapper. It includes a section explaining how to stucture HTML tags that build custom maps and link them to your Web pages
       (see http://www.discoverlife.org/nh/id/20q/20q_help.html#Map).
     • Find place -- is a large gazetteer that includes 7.26 million latitude-longitude/place-name combinations from 250 countries. The data for the U.S. contains 1.8 million points from the USGS-GNIS database. They allow users to pull up aerial photographs for most schools and churches. The 5.4 million point in the NIMA database cover countries other than the United States. Here we propose to integrate Topozone.com's U.S. geo-referenced street addresses into the Global Mapper's gazetteer. This addition will allow most users in the U.S. to input their street address to use an aerial photograph of their neighborhood.
       (see http://pick4.pick.uga.edu/mp/20m?act=find_place &w=720 &h=360 &r=.00004 &la=0 &lo=0).
     • Make map -- allows users to build custom maps and overlay species ditributions
       (see http://pick4.pick.uga.edu/mp/20m?act=make_map).
     • Demo -- demonstrates a global map that includes points from databases at the Missouri Botanical Garden, University of Georgia, and University of Illinois
       (see http://pick4.pick.uga.edu/mp/20m?kind=Eichhornia+crassipes, Annona+glabra, Quercus+nigra, Sarracenia+purpurea, Sarracenia+flava, Sarracenia+minor, Acrosathe+annulata; MEI,Taenogerella+elizabethae; MEI,Insect+Diversity+Project).
   • Topozone's technology is completely compliant with Open GIS Consortium Web Mapping Service (OGCWMS). The Mapper overlays points on these maps through a thin CGI request. It would be technically straight forward to combine layers from other NBII nodes into the Mapper, so long as they are OGCWMS compliant.
   • Topozone.com has the largest, most up-to-date, and accurate set of maps and aerial photographs anywhere on the Web. It serves on the order of 300,000 maps per day, many of them to the public for free. These maps are copyrighted to Maps a la Carte, Inc. Some of Topozone's premium services are subject to user fees. As part of the partnership to develop the Global Mapper, Topozone.com donates over $35,000 per year in maps and aerial photographs to Discover Life.
   • For compliant databases that provide unique identifiers with their point data, we add links on the maps to enable Web users to query data records associated with individual points. Currently we are doing this for data provided by databases at the Missouri Botanical Garden, the University of Georgia, and the University of Illinois.
   • The Global Mapper uses the NAD83 standard to plot points. We will require contributing databases to provide points in NAD83 or NAD27 standards and to specify which one they are using. The Global Mapper automatically switches from latitude-longitude to UTM coordinates at finer resolutions. Currently we accept points in either of these coordinate systems, but not in other ones.
   • We would prefer that partnering databases allow 20q to get points and associated records from them on the fly using HTTP GET or POST requests. 20q processes the data returned in various formats, including HTML, XML, and plain text. However, for databases that are not Web-enabled, but that are connected to the Internet, 20q can integrate data into the Global Mapper through direct requests to DBI compliant databases, such as Oracle and MySQL, after authorizing with a login name and password.
   • We envision extending the use of the Global Mapper to additional databases and also allowing users to contribute their observations to participating databases. We plan to build a Web-based, real-time monitoring system of invasive species and other things of concern.

4. Servers
   At no charge to users, we will serve the proposed guides, images, and maps through existing Discover Life servers into the foreseeable future.
   • Currently we have five Sun servers running at the University of Georgia, Athens, and one Linux server at the Agricultural Research Council, South Africa, that together served over 825,000 pages and images in October, 2003.
   • In 2003, Sun Microsystems Inc. gave The Polistes Foundation an equipment grant of over $200,000. This included a cluster of 20 storage disks and 10 processors that have been installed at Missouri Botanical Garden. Before the proposed project begins, this equipment will come on-line and mirror Discover Life's site at the University of Georgia. As part of Sun's gift, an additional server will also come on-line soon at the University of Georgia.
   • If at some point we are unable to continue this service, we will transfer the guides to a non-profit organization or government agency.

5. Copyright
   The PI and other contributors will retain ownership and exclusive copyright, with all rights reserved, to any illustrations, photographs, maps, or text they place in the guides or elsewhere on the Discover Life or associated Websites. The Polistes Corporation does the same for the 20q software that serves the guides, and Topozone.com, for the mapping software and services it provides.